How can I get the new Templates to work in Blender 2.79?
It looks like it doesn't work with Environment Variables at this moment because of this bug:
https://developer.blender.org/T52442

I hoped it should be solved by this fix:
https://developer.blender.org/rB2aa2bec43a7f1fa214833c73d033ae1785c600f3
... but it still does not work even in the most recent builds.

But regardless of Environment Variables, you should still be able to test your template by moving the bl_app_templates_user folder with your template to Blender's user directory c:\Users\yourusername\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\startup

So it will look like this





Make sure you no longer have a duplicate of your theme in the previous path (Blender program directory).